Simultaneous operation of opposing reaction mechanisms: The influence of matrix heterogeneity on post‐kinematic garnet crystallization in an inverted metamorphic sequence

2020 ◽  
Vol 38 (7) ◽  
pp. 743-769 ◽  
Author(s):  
Freya R. George ◽  
Fred Gaidies
Keyword(s):  
Reaction Mechanisms ◽  
Simultaneous Operation ◽  
Matrix Heterogeneity

Analyzing reactions of single mechanoenzyme molecules by light microscopy

1992 ◽  
Vol 50 (1) ◽  
pp. 426-427
Author(s):  
Jeff Gelles
Keyword(s):  
Image Processing ◽  
Reaction Mechanisms ◽  
Transient State ◽  
Nanometer Scale ◽  
Reaction Intermediates ◽  
Enzyme Molecule ◽  
Directed Movement ◽  
Enzyme Molecules ◽  
Individual Enzyme ◽  
Single Reaction

Mechanoenzymes are enzymes which use a chemical reaction to power directed movement along biological polymer. Such enzymes include the cytoskeletal motors (e.g., myosins, dyneins, and kinesins) as well as nucleic acid polymerases and helicases. A single catalytic turnover of a mechanoenzyme moves the enzyme molecule along the polymer a distance on the order of 10−9 m We have developed light microscope and digital image processing methods to detect and measure nanometer-scale motions driven by single mechanoenzyme molecules. These techniques enable one to monitor the occurrence of single reaction steps and to measure the lifetimes of reaction intermediates in individual enzyme molecules. This information can be used to elucidate reaction mechanisms and determine microscopic rate constants. Such an approach circumvents difficulties encountered in the use of traditional transient-state kinetics techniques to examine mechanoenzyme reaction mechanisms.

X-Ray Microanalysis of Nickel and Cobalt Intensified Peroxidase- Antiperoxidase For Verification of Reaction Sites

1985 ◽  
Vol 43 ◽  
pp. 468-469
Author(s):  
A. Angel ◽  
K. Miller ◽  
V. Seybold ◽  
R. Kriebel
Keyword(s):  
Reaction Mechanisms ◽  
Visual Discrimination ◽  
Osmium Tetroxide ◽  
Ultrastructural Level ◽  
Microscopic Level ◽  
Electron Microscopic Level ◽  
Electron Microscopic ◽  
X Ray ◽  
Insoluble Polymer ◽  
Cytochemical Reaction

Localization of specific substances at the ultrastructural level is dependent on the introduction of chemicals which will complex and impart an electron density at specific reaction sites. Peroxidase-antiperoxidase(PAP) methods have been successfully applied at the electron microscopic level. The PAP complex is localized by addition of its substrate, hydrogen peroxide and an electron donor, usually diaminobenzidine(DAB). On oxidation, DAB forms an insoluble polymer which is able to chelate with osmium tetroxide becoming electron dense. Since verification of reactivity is visual, discrimination of reaction product from osmiophillic structures may be difficult. Recently, x-ray microanalysis has been applied to examine cytochemical reaction precipitates, their distribution in tissues, and to study cytochemical reaction mechanisms. For example, immunoreactive sites labelled with gold have been ascertained by means of x-ray microanalysis.

Цифровая морфометрия разнокачественности семян овощных культур

2018 ◽  
Author(s):  
F.B. Musaev ◽  
N.S. Priyatkin ◽  
M.V. Arkhipov ◽  
P.A. Shchukina ◽  
A.F. Bukharov ◽  
...  
Keyword(s):  
Seed Quality ◽  
Image Analysis System ◽  
Flatbed Scanner ◽  
The Future ◽  
Scanned Images ◽  
Computer Morphometry ◽  
Analysis System ◽  
Matrix Heterogeneity ◽  
Relationship Of ◽  
Selection Of

Приведено описание разработанной авторами методики цифровой компьютерной морфометрии семян овощных культур на основе системы анализа изображений, состоящей из планшетного сканера и программного обеспечения для автоматических измерений. В основу метода положено представление о разнокачественности семян, обусловленной генетической неоднородностью самих семенных растений, используемых в промышленном семеноводстве. Физические свойства семян (их форма и линейные размеры) – основные параметры при определении их качества. Цифровые изображения семян получены при помощи планшетного сканера HP Sсanjet 200 на базе Агрофизического НИИ с использованием серийного программного обеспечения «Argus-BIO», производства ООО «АргусСофт» (г. Санкт-Петербург). Метод состоит из подбора контрастной подложки (фона) для сканирования семян с минимальными теневыми эффектами, калибровку программного обеспечения для привязки к истинным размерным величинам, подбор параметров измерений и автоматическое распознавание цифровых сканированных изображений семян. Представлены экспериментальные данные по морфометрии экологически разнокачественных семян фасоли овощной, матрикально разнокачественных семян укропа, пастернака и лука Кристофа. Семена укропа и пастернака, собранные из разных порядков ветвления семенного растения, значительно различались по величине линейных параметров. Наиболее показательный линейный параметр семян – площадь проекции. Предложенная авторами методика цифровой морфометрии, уже использована на практике и в перспективе может быть задействована в исследованиях экологической и матрикальной разнокачественности семян овощных культур. Так, она прошла апробацию на разнокачественных семенах пяти сортов фасоли овощной (Настена, Магура, Миробела, Морена, Бажена) полученных в пяти контрастных эколого-географических условиях среды (Москва, Белгород, Ставрополь, Омск, Горки) в 2011–2012 годах. В дальнейшем методика может быть использована для улучшения качества цифровых изображений семян, изучения разнокачественности семян в том числе и для совершенствования контроля за селекционным процессом. Кроме того, она применима для изучения взаимосвязи совокупности морфометрических характеристик семян и их посевных качеств.The description of the method of digital computer morphometry of vegetable seeds developed by the authors on the basis of the image analysis system consisting of a flatbed scanner and software for automatic measurements is given. The method is based on the idea of seed quality, due to the genetic heterogeneity of the seed plants used in industrial seed production. Physical properties of seeds (their shape and linear dimensions) are the main parameters in determining their quality. Digital image of the seed obtained using the flatbed scanner, HP Sсanjet 200 on the basis of the Agrophysical research Institute with serial software “Argus-BIO”, produced by LLC “Argussoft” (Saint-Petersburg). The method consists of selection of a contrast substrate (background) for scanning seeds with minimal shadow effects, calibration of software for binding to true size values, selection of measurement parameters and automatic recognition of digital scanned images of seeds. Experimental data on the morphometry of ecologically different-quality seeds of vegetable beans, matrix seeds of dill, Pasternak and Christoph onion are presented. Seeds of dill and parsnip, collected from different orders of branching of the seed plant, significantly differed in size of linear parameters. The most revealing linear parameter seed – area projection. The method of digital morphometry proposed by the authors has already been used in practice and in the future can be used in studies of ecological and matrix heterogeneity of vegetable seeds. So, it was tested on different quality seeds of five varieties of vegetable beans (Nastena, Magura, Mirobelа, Morena, Bazhenf) obtained in five contrasting environmental and geographical conditions (Moscow, Belgorod, Stavropol, Omsk, Gorki) in 2011-2012. In the future, the technique can be used to improve the quality of digital images of seeds, study of seed diversity, including to improve the control of the breeding process. In addition, it is applicable to study the relationship of the set of morphometric characteristics of seeds and their sowing qualities.

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

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